PDBsum entry: 1i7q

Lyase

PDB id: 1i7q

Contents

Protein chains

517 a.a. *

192 a.a. *

Ligands

BEZ ×2

PYR ×2

GLU ×2

Metals

_MG ×2

Waters ×1324

* Residue conservation analysis

PDB id:

1i7q

Name:

Lyase

Title:

Anthranilate synthase from s. Marcescens

Structure:

Anthranilate synthase. Chain: a, c. Synonym: anthranilate synthase trpe. Engineered: yes. Trpg. Chain: b, d. Synonym: anthranilate synthase trpg. Engineered: yes

Source:

Serratia marcescens. Organism_taxid: 615. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PQS)

Resolution:

1.95Å R-factor: 0.181 R-free: 0.246

Authors:

G.Spraggon,C.Kim,X.Nguyen-Huu,M.-C.Yee,C.Yanofsky,S.E.Mills

Key ref:

G.Spraggon et al. (2001). The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan. Proc Natl Acad Sci U S A, 98, 6021-6026. PubMed id: 11371633 DOI: 10.1073/pnas.111150298

Date:

10-Mar-01 Release date: 16-May-01

Protein chains

P00897  (TRPE_SERMA) -  Anthranilate synthase component 1

Seq: 519 a.a.

Struc: 517 a.a.*

Protein chains

P00900  (TRPG_SERMA) -  Anthranilate synthase component II

Seq: 193 a.a.

Struc: 192 a.a.*

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.4.1.3.27 - Anthranilate synthase.
• Pathway: Tryptophan Biosynthesis
• Reaction: Chorismate + L-glutamine = anthranilate + pyruvate + L-glutamate

Chorismate + L-glutamine (Bound ligand (Het Group name = GLU) matches with 90.00% similarity) = anthranilate (Bound ligand (Het Group name = BEZ) matches with 90.00% similarity) + pyruvate (Bound ligand (Het Group name = PYR) corresponds exactly) + L-glutamate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (6 terms)
• Biochemical function: catalytic activity (6 terms)

reference

DOI no: 10.1073/pnas.111150298

Proc Natl Acad Sci U S A 98:6021-6026 (2001)

PubMed id: 11371633

The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan.

G.Spraggon, C.Kim, X.Nguyen-Huu, M.C.Yee, C.Yanofsky, S.E.Mills.

ABSTRACT

The crystal structure of anthranilate synthase (AS) from Serratia marcescens, a mesophilic bacterium, has been solved in the presence of its substrates, chorismate and glutamine, and one product, glutamate, at 1.95 A, and with its bound feedback inhibitor, tryptophan, at 2.4 A. In comparison with the AS structure from the hyperthermophile Sulfolobus solfataricus, the S. marcescens structure shows similar subunit structures but a markedly different oligomeric organization. One crystal form of the S. marcescens enzyme displays a bound pyruvate as well as a putative anthranilate (the nitrogen group is ambiguous) in the TrpE subunit. It also confirms the presence of a covalently bound glutamyl thioester intermediate in the TrpG subunit. The tryptophan-bound form reveals that the inhibitor binds at a site distinct from that of the substrate, chorismate. Bound tryptophan appears to prevent chorismate binding by a demonstrable conformational effect, and the structure reveals how occupancy of only one of the two feedback inhibition sites can immobilize the catalytic activity of both TrpE subunits. The presence of effectors in the structure provides a view of the locations of some of the amino acid residues in the active sites. Our findings are discussed in terms of the previously described AS structure of S. solfataricus, mutational data obtained from enteric bacteria, and the enzyme's mechanism of action.

Selected figure(s)

Figure 2.
Fig. 2. Structure of the AS of S. marcescens. (a) Ribbon diagram of the AS oligomer, TrpG subunits shown in blue, TrpE subdomain I shown in green subdomain II in yellow. Striped regions correspond to additional structure in S. marcescens compared with that of S. solfataricus. Glutamyl, benzoate, pyruvate, and tryptophan are shown as CPK models. (b) Stereo diagram of the heterodimer; TrpG shown in lilac, TrpE in black; regions of TrpG that move on addition of tryptophan relative the C-crystal are shown in red, whereas those of TrpE are in yellow; residues important to the CA-binding pocket (G328, T329, H398, G485) are shown as light blue balls, residues involved in pyruvate interactions (Y449, R469, G483) are in purple, residues involved in magnesium coordination (E358,361, E495, E498) are colored light purple, magnesium ion in orange, water molecules in dark blue, Trp-binding residues (S40, P291, M293, V453, Y455) are light green, and residues involved in glutamine binding (P57, G58, G60, C85, L86, Q89, S135, S136) are in green. Benzoate, pyruvate, magnesium, and glutamyl are shown as ball-and-stick figures. Produced by BOBSCRIPT and RASTER 3D (39-42).

Figure 3.
Fig. 3. Substrate product and Trp-binding sites of the AS molecule. Carbon atoms are dark gray, nitrogen blue, and oxygen red. Electrostatic and hydrogen-bond interactions are shown as black dotted lines. (a) Binding residues for glutamyl thioester intermediate of TrpG. Glutamyl moiety drawn with cyan bonds. A [A]-weighted F[o] F[c] map contoured at 3.5 SD is shown in transparent blue. (b) CA-binding pocket, anthranilate, and pyruvate are drawn with dark red bonds, magnesium ion in orange, ordered waters in cyan. A [A]-weighted F[o] F[c] map contoured at 3.0 SD is shown in transparent green. (c) Trp-binding pocket, tryptophan shown in green. (d) Conformational states associated with anthranilate, pyruvate, and Trp-bound forms. The molecule is viewed with the molecular 2-fold perpendicular to the page (i.e., perpendicular to the view in Fig. 2a). TrpG subunits shown in transparent blue, helixes and loops involved in heterotetramer rearrangement shown as rods, C-crystal representation shown in green rearrangement in the T-crystal, shown in red. Tryptophan is shown as CPK model in yellow. Produced by BOBSCRIPT and RASTER 3D (39-42).

Figures were selected by an automated process.